A process can open a FIFO in non-blocking mode. In this case, opening for read only will succeed even if noone has opened on the write side yet; opening for write only will fail with ENXIO (no such device or address) unless the other end has already been opened. You should open this one in the 'client'.
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alexdobin commented on Jul 16, 2019
please try to create a fifo file with mkfifo tmp.fifo in the run directory, if it works, than the problem is somewhere else. Also, please try to uncompress the fastq file first and map without the --readFilesCommand option, which will not use fifo files.
alexdobin commented on Jul 22, 2019
thanks a lot for the investigations. I can try to add the shebang line to the readsCommand_read1/2 scripts, as it seems to me the most common cause for the execlp errno=8 'Exec format error'.
alexdobin commented on Jul 22, 2019
I was looking at the code and realized that this had been implemented already. :) Please try --sysShell /bin/sh (or whatever shell works as shebang on your system). This will add #!/bin/sh to the readsCommand_read1/2 scripts.
